- RCSBTools - Class in IMPACT_S
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Basic functionality for downloading PDB files from RCSB website.
- RCSBTools() - Constructor for class IMPACT_S.RCSBTools
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- readCSVFile() - Method in class IMPACT_S.ResultsView
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Read active CSV file.
- readMSAFile() - Method in class IMPACT_S.AlignmentEditor
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Read sequences from specified file and format.
File and Format instantiated through the constructor method.
- readMSAfile() - Method in class IMPACT_S.FileFormatConverter
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Read MSA file for instantiated source file and format.
- readSeqsFormatFile() - Method in class IMPACT_S.FileFormatReader
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Read MSA file for instantiated source file and format.
- RELFileLocKey - Static variable in class IMPACT_S.DatamonkeyTP
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REL input file key.
- RELmodel - Static variable in class IMPACT_S.DatamonkeyTP
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REL model code = 2.
- removeCanceledTMPFls(Utilities, String, boolean) - Method in class IMPACT_S.AlignmentEditor
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Remove temporary files created for PhyML execution resulting from cancelation.
- renameFile(String, String, boolean) - Method in class IMPACT_S.Utilities
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Copies content from source file to destination file.
This way creating a rename operation.
This was created to overcome limitations of File.renameTo() method.
Replaces any destination file that may exist.
- renamePhymlFiles(Utilities, String, boolean) - Method in class IMPACT_S.AlignmentEditor
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Rename PhyML files created on directory chosen to
the name specified by user.
- replaceExtBy(String, String) - Method in class IMPACT_S.Utilities
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Replace extension with new given extension.
- Results3DDirName - Static variable in class IMPACT_S.Utilities
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GUI Results tab directory name.
- ResultsDataKey - Static variable in class IMPACT_S.Utilities
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GUI Results & 3D data location
- ResultsN3DTP - Class in IMPACT_S
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Class to handle necessary computation and data storage for general or final results.
Results from previous tabs and from resources like Jmol and Swiss Model.
- ResultsN3DTP(Utilities) - Constructor for class IMPACT_S.ResultsN3DTP
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Initialize ResultsN3D with empty fields.
- ResultsView - Class in IMPACT_S
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Implementation of several methods to allow reading Comma Separated Values (CSV) files.
- ResultsView() - Constructor for class IMPACT_S.ResultsView
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Constructor for instantiation of files later.
- ResultsView(String, String) - Constructor for class IMPACT_S.ResultsView
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Constructor for file1 and file2 instantiation.
- retrieveFEL(double) - Method in class IMPACT_S.DatamonkeyTP
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Retrieve FEL method Positive and Negative selection.
- retrieveFUBAR(double) - Method in class IMPACT_S.DatamonkeyTP
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Retrieve FUBAR method Positive and Negative selection.
- retrieveMEME(double) - Method in class IMPACT_S.DatamonkeyTP
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Retrieve MEME method Positive selection.
- retrieveREL(double) - Method in class IMPACT_S.DatamonkeyTP
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Retrieve REL method Positive and Negative selection.
- retrieveSLAC(double) - Method in class IMPACT_S.DatamonkeyTP
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Retrieve SLAC method Positive and Negative selection.